DNASeq_align

Introduction

The DNASeq alignment pipeline was included in the RcwlPipelines package. It majorly includes two steps:

• bwa alignment by read groups.
• Merge by samples and markduplicates.

Here is the short summary and step plots.

suppressPackageStartupMessages(library(Rcwl))
library(RcwlPipelines)
data("alignMerge")

short(alignMerge)

inputs:
- idBam
- RG
- threads
- Ref
- FQ1s
- FQ2s
outputs:
- oBam
- matrix
- Idx
- stat
steps:
- bwaAlign
- mergeBamDup

plotCWL(alignMerge)

1. BWA alignment

plotCWL(runs(alignMerge)$bwaAlign)

2. Merge and markduplicates

plotCWL(runs(alignMerge)$mergeBamDup)

Prepara data

Here is an example of two samples. The “sample1” have two lanes of sequences and the “sample2” only has one pair of reads. The lists of reads1 fq1, reads2 fq2, read groups and output BAM names are defined in the inputList. The reference genome and number of threads to run the job are defined in the shared options, paramList.

fq1 <- list(sample1 = list("data/fq1_1.fq", "data/fq2_1.fq"),
            sample2 = list("data/fq1_1.fq"))
fq2 <- list(sample1 = list("data/fq1_2.fq", "data/fq2_2.fq"),
            sample2 = list("data/fq1_2.fq"))
rgs <- list(sample1 = list("@RG\\tID:sample1.1\\tSM:sample1", "@RG\\tID:sample1.2\\tSM:sample1"),
            sample2 = list("@RG\\tID:sample2.1\\tSM:sample2"))
samples <- list(sample1 = "sample1.bam", sample2 = "sample2.bam")

inputList <- list(idBam = samples, RG= rgs, FQ1s = fq1, FQ2s = fq2) 
paramList <- list(threads = 2,
                  Ref = "/rpcc/bioinformatics/reference/current/hs37d5.fa")

DNA alignment pipeline

res <- runCWLBatch(alignMerge, wdir = "output/BAM",
                   inputList = inputList, paramList = paramList,
                   BPPARAM = BatchtoolsParam(workers = 2, cluster = "sge",
                                             template = "/rpcc/bioinformatics/sge.tmpl",
                                             resources = list(jobname="bwa",
                                                              threads = 2,
                                                              queue = "all.q")))

Outputs:

dir("output/BAM/sample1")

[1] "sample1.bam"          "sample1.bam.bai"      "sample1.flagstat.txt"
[4] "sample1.markdup.txt" 

Session information

sessionInfo()

R version 3.5.2 Patched (2018-12-31 r75935)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.4 (Final)

Matrix products: default
BLAS: /home/qhu/usr/R-3.5/lib64/R/lib/libRblas.so
LAPACK: /home/qhu/usr/R-3.5/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] RcwlPipelines_0.0.0.9000 jsonlite_1.6            
[3] BiocParallel_1.16.2      Rcwl_0.99.7             
[5] S4Vectors_0.20.1         BiocGenerics_0.28.0     
[7] yaml_2.2.0               workflowr_1.1.1         

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0         tidyr_0.8.2        visNetwork_2.0.5  
 [4] prettyunits_1.0.2  assertthat_0.2.0   rprojroot_1.3-2   
 [7] digest_0.6.18      plyr_1.8.4         R6_2.3.0          
[10] backports_1.1.3    evaluate_0.12      highr_0.7         
[13] ggplot2_3.1.0      pillar_1.3.1       rlang_0.3.0.1     
[16] progress_1.2.0     lazyeval_0.2.1     rstudioapi_0.8    
[19] data.table_1.11.8  whisker_0.3-2      R.utils_2.7.0     
[22] R.oo_1.22.0        checkmate_1.8.5    rmarkdown_1.11    
[25] DiagrammeR_1.0.0   downloader_0.4     readr_1.3.1       
[28] stringr_1.3.1      htmlwidgets_1.3    igraph_1.2.2      
[31] munsell_0.5.0      compiler_3.5.2     influenceR_0.1.0  
[34] rgexf_0.15.3       xfun_0.4           pkgconfig_2.0.2   
[37] htmltools_0.3.6    tidyselect_0.2.5   gridExtra_2.3     
[40] tibble_1.4.2       batchtools_0.9.11  XML_3.98-1.16     
[43] viridisLite_0.3.0  crayon_1.3.4       dplyr_0.7.8       
[46] withr_2.1.2        R.methodsS3_1.7.1  rappdirs_0.3.1    
[49] grid_3.5.2         gtable_0.2.0       git2r_0.23.0      
[52] magrittr_1.5       scales_1.0.0       stringi_1.2.4     
[55] debugme_1.1.0      viridis_0.5.1      bindrcpp_0.2.2    
[58] brew_1.0-6         RColorBrewer_1.1-2 tools_3.5.2       
[61] glue_1.3.0         purrr_0.2.5        hms_0.4.2         
[64] Rook_1.1-1         colorspace_1.3-2   base64url_1.4     
[67] knitr_1.21         bindr_0.1.1